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Fix zero-padded integer metadata conflicts #1267

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Fix zero-padded integer metadata conflicts #1267

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10 changes: 9 additions & 1 deletion src/bids/layout/index.py
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Original file line number Diff line number Diff line change
Expand Up @@ -507,7 +507,15 @@ def create_association_pair(src, dst, kind, kind2=None):
# Skip pairs that were already found in the filenames
if tag_string in all_tags:
file_val = all_tags[tag_string]
if str(md_val) != file_val:
entity = all_entities.get(md_key)
values_match = str(md_val) == file_val
if (
entity is not None
and entity._dtype == 'int'
and not isinstance(md_val, bool)
):
values_match = entity._astype(file_val) == md_val
if not values_match:
msg = (
"Conflicting values found for entity '{}' in "
"filename {} (value='{}') versus its JSON sidecar "
Expand Down
32 changes: 32 additions & 0 deletions src/bids/layout/tests/test_layout.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@

from bids.exceptions import (
BIDSChildDatasetError,
BIDSConflictingValuesError,
BIDSDerivativesValidationError,
BIDSValidationError,
NoMatchError,
Expand Down Expand Up @@ -965,6 +966,37 @@ def test_indexing_tag_conflict(tests_dir):
assert 'run' in str(exc.value)


@pytest.mark.parametrize('metadata_run', [1, 1.0])
def test_indexing_zero_padded_entity_matches_numeric_metadata(tmp_path, metadata_run):
(tmp_path / 'dataset_description.json').write_text(
json.dumps({'Name': 'test', 'BIDSVersion': '1.10.0'})
)
func_dir = tmp_path / 'sub-01' / 'func'
func_dir.mkdir(parents=True)
bold_file = func_dir / 'sub-01_task-rest_run-01_bold.nii.gz'
bold_file.touch()
bold_file.with_suffix('').with_suffix('.json').write_text(json.dumps({'run': metadata_run}))

layout = BIDSLayout(tmp_path)

assert layout.get(run=1, suffix='bold', extension='.nii.gz')


@pytest.mark.parametrize('metadata_run', [2, 1.5, True, '1'])
def test_indexing_zero_padded_entity_rejects_conflicting_metadata(tmp_path, metadata_run):
(tmp_path / 'dataset_description.json').write_text(
json.dumps({'Name': 'test', 'BIDSVersion': '1.10.0'})
)
func_dir = tmp_path / 'sub-01' / 'func'
func_dir.mkdir(parents=True)
bold_file = func_dir / 'sub-01_task-rest_run-01_bold.nii.gz'
bold_file.touch()
bold_file.with_suffix('').with_suffix('.json').write_text(json.dumps({'run': metadata_run}))

with pytest.raises(BIDSConflictingValuesError, match="entity 'run'"):
BIDSLayout(tmp_path)


def test_get_with_wrong_dtypes(layout_7t_trt):
"""Test automatic dtype sanitization."""
l = layout_7t_trt
Expand Down